Stockton DID have a better shooting %, no? He did not have a better 3pt% or ft%, though.
Many of the offenses Nash ran (especially during his zenith) were geared towards getting Nash shots (and threes, to boot). Whereas, the Offenses Stockton played in weren't geared towards getting John a shot (note: they were, however, geared towards John making a pass-which allowed John to amass otherworldly assist numbers).
I do think there are legitimate arguments to whether Nash was a better player than Stockton. However, I have major issues with anyone that thinks Nash was a better passer than Stockton. I basically don't think they saw Stockton at his peak from 88 through the early 90's.
Finally, I would have loved to have seen Stockton play (offensively, at least) under the rules that Nash peaked under. The changes in rules make comparing perimeter players from Stockton's era to now (and Nash's time) almost impossible (but still fun).